rs2224434

Variant names:

• chr4-73780598-A-C
• rs2224434
• ENST00000779090.1:n.210-2868T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000779090.1(ENSG00000301475):​n.210-2868T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.532 in 152,100 control chromosomes in the GnomAD database, including 23,440 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.53 (23440 hom., cov: 33)
• Consequence: ENSG00000301475 ENST00000779090.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.257
• Publications: 3 publications found

Genes affected

ENSG00000301475 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.774 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000779090.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000301475	ENST00000779090.1		n.210-2868T>G		intron	N/A
	ENSG00000301475	ENST00000779091.1		n.116-2868T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.532 AC: 80850 AN: 151984 Hom.: 23402 Cov.: 33

Gnomad AFR AF: 0.781

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.523

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.532 AC: 80940 AN: 152100 Hom.: 23440 Cov.: 33 AF XY: 0.522 AC XY: 38801 AN XY: 74348

African (AFR) AF: 0.781 AC: 32412 AN: 41486

American (AMR) AF: 0.421 AC: 6427 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.422 AC: 1463 AN: 3470

East Asian (EAS) AF: 0.378 AC: 1959 AN: 5188

South Asian (SAS) AF: 0.399 AC: 1923 AN: 4822

European-Finnish (FIN) AF: 0.392 AC: 4143 AN: 10570

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.456 AC: 31021 AN: 67986

Other (OTH) AF: 0.522 AC: 1101 AN: 2110

Alfa AF: 0.472 Hom.: 10522

Bravo AF: 0.547

Asia WGS AF: 0.409 AC: 1422 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.8
DANN	Benign	0.59
PhyloP100		-0.26

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2224434;

hg19: chr4-74646315;